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Re: Clade II

        I'm going to try to keep this brief, as I do not have time to get
dragged into a long debate...
Jeffrey Martz wrote:
>I feel these functions were confused in the debate on cladistics in November,
>so I want to spell them out now:
        Confused by you.  I tried very very hard to make the difference
clear.  It is gratifying to see that you are clear on this now!

        This is "cladistics" sensu stricto, or "cladistic analysis", or
"phylogenetic analysis" or whathaveyou.  This is what we mean when we say

        This is a seperate sister-discipline, called Phylogenetic Taxonomy.
Please call it this, and do not lump it under cladistics.

        Rather than quote extensively, I give you the following ref:
        De Queiroz, K., and Gauthier, J. 1990, Phylogeny as a central
principle in taxonomy: phylogenetic definitions of taxon names. Systematic
Zoology, 39:307-322
        If you read this argue, and feel that you are well enough versed in
philosophy, you may continue to debate this point.  Are you up on your

>How could any grouping of species, regardless of the criteria, ever be
"real"? >CLADISTS set the rules that groups must begin with a node and end
with >extinction (or the  present day- more on that later), not Nature.
        You miss the point.  If I can assume that there is a common ancestor
of any group, I can say that there exists a set of animals which decended
from that ancestor.  Read the ref.

>How is common descent any more real than the possession of scales or the
>absense of hair, or the endothermic or ectothermic metabolism?  Cladistic
rules >may limit the potential number of groups more that paraphyly, but it
doesn't >make these groups any more real.   
        These things are all real, but they do not form real groups of
animals according to the guiding paradigm of modern biology (ie. evolution
by natural selection).  They for groups which are frequently based on
similarity, not phylogeny, and are not, as groups, real, even if the
characters used to define them are.

        This is for others to debate.  At the species level, it may be
impossible to form monophyletic groups.  Why should this prevent us from
grouping those groups into monophyletic assembleges which are real entities?
>     Every single paraphyleic group that exists, as diagnosed in the
        Yes, and if you included it's decendants, it still would be.  You
are looking at it the wrong way.  Don't ask why you can't make a parphyletic
group because it was one monophyletic, ask yourself where the sense is in
excluding some of the decendants of a once monophyletic group, thus making
it paraphyletic.  Why would you do this?

>If clades are "real" and paraphyletic groups are not, what does that mean
for >fish and reptiles?  They used to be real, but now they're not?
        They are clearly still real if you include all of their decendants.
You really need to get out of the Linnean mindset.  A clade formed by the
common ancestor of, oh, say, _Ichthyostega_ and _Carcharodon_ and all of its
decendants is still a clade, at any time, no matter whether you are in the
Permian, the Jurassic, or the Recent.  A group of animals determined by a
set of characteristics (eg. "fish") MAY be a clade at one of these points,
but is not necessarily one.  So, yes, "fish" and "reptiles" (sensu Martz)
were probably real once (judged by composition, as including the common
ancestor and all of the decendants), but are not any more, because the
concept of "fish" and "reptile" are artificial, whereas the clade
{+_Ichthyostega_, + _Carcharodon_} is a RECOGNITION OF A REAL GROUP, and
thus will always be real.

>     Paraphyletic clades are therefore NOT just definable by the absense
>of an apomorphy, but by the PRESENCE of a trait no longer possessed by the
>descendant group.
        If you wish to have your taxa have evolutionary meaning, then they
must be devined (but not defined!) on the basis of shared derived
characters, which you yourself have admitted is the best way to elucidate
phylogeny.  If you make such paraphyletic groups, they are neither real
entities, nor are they useful for any discussion of phylogeny, except
inasmuch as providing an example of the plesiomorhpic state of the excluded
("advanced") clade.
        Note that what you say in bold above is true, but since the presence
of a plesiomorphic character state is not _unique_ to the taxa you place in
your taxon, the presence of that state is meaningless for any purpose other
than classification.

>The fact that a descent group possesses the apomorphy is no more real then
the >fact that the ancestor has the ancestral trait.      
        As I have tried repeatedly to emphasize, Phylogenetic Taxa are not
defined by character states.  Character states are not what makes them real.

        OF COURSE paraphyletic groups (above the species level) are
convenient, sometimes very convenient, but they are not real groups, nor can
they be construed as fundamental evolutionary units.  They can still be
useful when one wishes to exclude some animals from analysis, but this does
not make them useful as taxa.  There is no reason you cannot use them, but
don't pretend that they are real groups, and they have no place in
Phylogenetic Taxonomy.

        However, cladistics is concerned with determining phylogeny in terms
of shared DERIVED characters, and Phylogenetic Taxonomy (PT) is concerned
with elucidating the phylogeny so determined.  The most succinct thing I can
say in response to this statement is "so what?"  PT is not concerned with
characters in common, it is concerned with phylogeny.

>    Monophyletic clades are defined by common descent, not greater
>similarity.  For an example, look at this cladogram:
        Good, feel the truth flow within you... 
>In all cases, A, B, and D share important aspects of behavior, metablism
[sic], >anatomy, and/or physiology than D does with C. 
        Which can be easily summed up as them retaining the retentiion of
the plesiomorphic state.  Note that by explaining it this way, we emphasize
the EVOLUTIONARY aspects of the relationships and de-emphasize the
SUPERFICIAL aspects (such as metabolism, behavior).  this is only just, as
EVOLUTION is the central paradigm of biology, and other elements of biology
should be discussed *in the context of evolution*.
        This certainly is sufficient answer to the Mayr quote.  The most
important aspect of evolution is the description of phylogeny.  How else are
we to determine the nature of adaptation (especially convergence and
parrallelism) without first couching our arguments in the context of
phylogeny?  Which is a more useful statement:
        "Some members of taxon A showed a tendancy towards developing
characteristics of taxon B, until one of them made the jump and was the
first member of taxon B." or
        "Amongst clade A, several clades developed adaptations towards
B-ness.  Clades C and D developed thier adaptations in paralell, while E was
a member of D which encroached closely on the state of B.  B itself arose
from C, and the interesting thing is how the plesiomorphic B-ness
adaptations of C were far less like those of members of B, although the
adaptations of E are almost identical to B."

>     These things may be (somewhat) separate from phylogeny, but
>why do it have to be seperate from taxonomy?  As evolutionists, we are
>interested in these subjects.  Who said, and WHY, that phylogenetic
>relationships were the be all and end all of taxonomy?    
        The central paradigm of each science is the structure around which
it's systematics is based.  In biology we have the unique oppurtunity to
convert from an abstract classification system to a system which both
represents the workings of the natural world, and is fundamentally useful in
discussions of the central paradigm of the science.  WHY would we choose to
base our systematics on things which are easily determined and very likely
to be homoplastic, when we can refine the focus of it and make it something
truly useful?

Stan Friesen wrote:
>Also, given that according to the rules of nomenclature all species
>must be assigned to a genus, then either the genus containing the
>ancestral species is paraphyletic or all living things belong to one
        Practicioners of PT do not tend to recognize paraphyletic genera.
IF the genus gives rise to a non-member, the genus is split.  Genera are
commonly terminal taxa, on the assumption that they are monophyletic.  You
are alwyas free to test this assumption

Gautam Majumdar wrote
>This is absolutely right. You classify a group (of anything) for a purpose 
>and select your criteria accordingly. Each such classification is valid in 
>its own context.
        Read the ref above.  PT is not a classification, it is a description
of the natural world.  Make up any sort of classification you want.  PT goes
beyond this.
>[snip]  In that context it is a perfectly valid and better classification
than >cladistics.
        And we are not bear-hunters, but biologists (of a sort), and the
most useful thing our "classification" can do is elucidate the fundamentals
of our central paradigm.  Thus, PT is the best option.

| Jonathan R. Wagner                    "You can clade if you want to,     |
| Department of Geosciences              You can leave your friends behind |
| Texas Tech University                  Because your friends don't clade  |
| Lubbock, TX 79409                               and if they don't clade, |
|       *** wagner@ttu.edu ***           Then they're no friends of mine." |
|           Web Page:  http://faraday.clas.virginia.edu/~jrw6f             |